# shrinkt.st: Calculate 'Shrinkage t' Statistic In tileHMM: Hidden Markov Models for ChIP-on-Chip Analysis

## Description

Calculate the ‘shrinkage t’ statistic (Opgen-Rhein and Strimmer, 2007).

## Usage

 `1` ```shrinkt.st(X, L, h0.mean = 0, ...) ```

## Arguments

 `X` Data matrix. Rows correspond to variables (probes) and columns to samples. `L` Design vector. Indicating treatment (1) and control (2) samples. If no control samples are given a one sample t test is carried out. `h0.mean` If no control samples are provided the treatment mean is compared to this value in a one sample t test. `...` Further arguments to be passed to and from other methods.

## Value

An object of class "`shrinkage`" containing the test statistics.

## Note

This method uses the `shrinkt.stat` method from package `st`.

Peter Humburg

## References

Opgen-Rhein, R., and K. Strimmer 2007. Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach. Statist. Appl. Genet. Mol. Biol. 6:9. http://www.bepress.com/sagmb/vol6/iss1/art9/

`shrinkt.stat`
 ``` 1 2 3 4 5 6 7 8 9 10``` ```## generate some data X <- matrix(nrow = 100, ncol = 6) X[ , 1:3] <- apply(X[ , 1:3], 1, rnorm, mean = rnorm(1, mean = 2, sd = 2), sd = rchisq(1, df = 2)) X[ , 4:6] <- apply(X[ , 4:6], 1, rnorm, mean = rnorm(1, mean = 0, sd = 1), sd = rchisq(1, df = 2)) L <- c(1, 1, 1, 2, 2, 2) ## compute shrinkage t statistic st.stat <- shrinkt.st(X, L) ```